SMTL ID : 1ofy.1

THREE DIMENSIONAL STRUCTURE OF THE REDUCED FORM OF NINE-HEME CYTOCHROME C AT PH 7.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

18 x HEC: HEME C(Covalent)

HEC.1: 16 residues within 4Å: Chain A: S.8, A.10, P.11, I.14, M.16, F.35, H.37, H.40, I.44, N.46, C.47, C.50, H.51, P.56, S.58 Ligands: HEC.3 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:A.10, A:I.14, A:F.35, A:H.40, A:I.44, A:I.44, A:P.56 Metal complexes: A:H.37, A:H.51 HEC.2: 20 residues within 4Å: Chain A: C.50, H.52, T.53, D.55, V.57, S.58, C.59, T.61, C.62, H.63, E.70, G.71, N.72, R.78, A.79, M.80, I.85, R.88, P.94, V.95 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:V.57, A:A.79, A:I.85, A:P.94 Water bridges: A:R.88, A:R.88 Salt bridges: A:R.78, A:R.88, A:R.88 Metal complexes: A:H.52, A:H.63 HEC.3: 23 residues within 4Å: Chain A: M.16, V.33, F.35, N.36, I.39, H.40, K.43, I.44, T.49, C.50, V.95, S.96, C.97, C.100, H.101, Q.104, T.129, C.130, K.212, L.213, A.216 Ligands: HEC.1, HEC.5 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:V.33, A:F.35, A:I.44, A:T.49, A:V.95, A:L.213, A:L.213, A:A.216 Hydrogen bonds: A:K.212 Water bridges: A:N.36, A:N.36, A:K.43, A:K.43, A:Q.166 Salt bridges: A:K.43 pi-Stacking: A:F.35 Metal complexes: A:H.40, A:H.101 HEC.4: 22 residues within 4Å: Chain A: E.102, T.105, R.108, E.110, C.111, C.114, H.115, V.118, T.119, P.120, K.121, W.126, L.204, I.208, D.211, L.213, A.214, F.217, H.218, I.223, L.224, T.227 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:T.105, A:V.118, A:V.118, A:P.120, A:L.204, A:I.208, A:I.208, A:D.211, A:L.213, A:A.214, A:F.217, A:F.217, A:F.217, A:I.223, A:L.224 Hydrogen bonds: A:T.119, A:K.121 Water bridges: A:K.121, A:R.122 Salt bridges: A:H.115, A:K.121 Metal complexes: A:H.115, A:H.218 HEC.5: 23 residues within 4Å: Chain A: M.16, F.17, P.18, A.29, M.30, K.31, P.32, V.33, L.76, M.80, H.81, C.97, H.101, R.122, W.126, C.127, C.130, H.131 Chain B: R.231, P.239, S.243, C.244 Ligands: HEC.3 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:M.16, A:P.18, A:V.33, A:M.80, A:W.126, A:W.126, A:W.126 Hydrogen bonds: A:F.17, A:M.30, A:M.30, A:V.33, B:S.243 Salt bridges: A:H.131 Metal complexes: A:H.81, A:H.131 HEC.6: 21 residues within 4Å: Chain A: V.172, A.177, P.178, V.181, I.183, F.195, H.197, L.201, L.224, C.225, C.228, H.229, S.235, L.236, P.238, K.240, C.241, Y.263 Chain B: K.26, A.28 Ligands: HEC.8 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:V.172, A:A.177, A:P.178, A:F.195, A:L.201, A:L.201, A:L.236, B:K.26, B:A.28 Hydrogen bonds: A:C.241 Water bridges: A:K.240, B:K.26, B:K.26 Salt bridges: A:K.240, B:K.26 Metal complexes: A:H.197, A:H.229 HEC.7: 15 residues within 4Å: Chain A: C.228, H.229, H.230, R.231, K.240, C.241, C.244, H.245, G.255, R.256, P.257, A.262, L.265, Q.266 Ligands: GOL.21 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:R.256, A:P.257, A:A.262, A:L.265 Water bridges: A:I.117, A:H.230, A:R.231, A:R.231 Salt bridges: A:H.230, A:R.231, A:R.231 Metal complexes: A:H.230, A:H.245 HEC.8: 24 residues within 4Å: Chain A: C.114, I.117, I.183, S.193, F.195, T.196, R.199, H.200, S.203, L.204, R.207, C.228, Q.266, C.267, C.270, H.271, M.274, V.276, R.278, P.279, T.286, C.287 Ligands: HEC.6, HEC.9 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:I.117, A:I.183, A:F.195, A:L.204, A:V.276, A:T.286 Hydrogen bonds: A:T.196, A:S.203 Salt bridges: A:R.199, A:H.200, A:R.207 Metal complexes: A:H.200, A:H.271 HEC.9: 23 residues within 4Å: Chain A: I.183, D.184, A.185, L.186, A.187, D.188, K.189, Y.190, S.193, M.260, Y.263, H.264, C.267, M.268, H.271, P.279, R.280, D.281, D.283, C.284, C.287, H.288 Ligands: HEC.8 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:I.183, A:I.183, A:L.186, A:Y.263, A:Y.263, A:P.279 Hydrogen bonds: A:L.186, A:D.188, A:K.189, A:Y.190 Water bridges: A:Y.190 Metal complexes: A:H.264, A:H.288 HEC.12: 16 residues within 4Å: Chain B: S.8, A.10, I.14, M.16, F.35, H.37, H.40, I.44, N.46, C.47, C.50, H.51, P.56, S.58, C.59 Ligands: HEC.14 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:A.10, B:F.35, B:F.35, B:I.44, B:P.56 Hydrogen bonds: B:S.58, B:C.59 Water bridges: B:S.60 Metal complexes: B:H.37, B:H.51 HEC.13: 20 residues within 4Å: Chain B: C.50, H.52, T.53, V.57, S.58, C.59, T.61, C.62, H.63, E.70, G.71, N.72, I.74, R.78, A.79, M.80, I.85, R.88, P.94, V.95 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:V.57, B:N.72, B:I.74, B:A.79, B:I.85, B:P.94, B:P.94 Water bridges: B:A.86, B:R.88 Salt bridges: B:R.78, B:R.88, B:R.88 Metal complexes: B:H.52, B:H.63 HEC.14: 24 residues within 4Å: Chain B: M.16, V.33, F.35, N.36, I.39, H.40, K.43, I.44, T.49, C.50, V.95, S.96, C.97, C.100, H.101, Q.104, T.129, C.130, Q.166, K.212, L.213, A.216 Ligands: HEC.12, HEC.16 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:V.33, B:F.35, B:F.35, B:I.39, B:K.43, B:I.44, B:T.49, B:V.95, B:L.213, B:L.213, B:A.216 Hydrogen bonds: B:K.212 Water bridges: B:N.36, B:K.43, B:Q.166, B:K.212, B:K.212 Salt bridges: B:K.43, B:K.212 pi-Stacking: B:F.35 Metal complexes: B:H.40, B:H.101 HEC.15: 22 residues within 4Å: Chain B: E.102, T.105, R.108, E.110, C.111, C.114, H.115, V.118, P.120, K.121, R.122, W.126, L.204, I.208, D.211, L.213, A.214, F.217, H.218, I.223, L.224, T.227 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:T.105, B:E.110, B:P.120, B:L.204, B:I.208, B:I.208, B:D.211, B:L.213, B:A.214, B:F.217, B:F.217, B:F.217, B:I.223, B:L.224 Hydrogen bonds: B:E.102, B:K.121 Water bridges: B:E.102, B:T.105 Salt bridges: B:K.121, B:R.122, B:K.220 Metal complexes: B:H.115, B:H.218 HEC.16: 26 residues within 4Å: Chain A: R.231, S.232, P.239, S.243, C.244 Chain B: M.16, F.17, P.18, A.29, M.30, K.31, P.32, V.33, L.76, M.80, H.81, C.97, H.101, R.122, W.126, C.127, C.130, H.131 Ligands: GOL.11, HEC.14, GOL.21 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:M.16, B:P.18, B:V.33, B:V.33, B:M.80, B:W.126, B:W.126, B:W.126 Hydrogen bonds: B:F.17, B:M.30, B:M.30, B:V.33, A:S.243 Salt bridges: B:H.131 Metal complexes: B:H.81, B:H.131 HEC.17: 20 residues within 4Å: Chain A: K.26 Chain B: V.172, A.177, P.178, V.181, I.183, F.195, H.197, L.201, L.224, C.225, C.228, H.229, S.235, L.236, P.238, K.240, C.241, Y.263 Ligands: HEC.19 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:V.172, B:A.177, B:P.178, B:V.181, B:I.183, B:F.195, B:L.201, B:L.236, A:K.26 Hydrogen bonds: B:C.241 Water bridges: B:K.180 Metal complexes: B:H.197, B:H.229 Salt bridges: A:K.26 HEC.18: 14 residues within 4Å: Chain B: C.228, H.229, H.230, R.231, P.239, K.240, C.241, C.244, H.245, R.256, P.257, A.262, L.265, Q.266 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:P.239, B:R.256, B:P.257, B:A.262, B:L.265, B:Q.266 Water bridges: B:I.117, B:I.117, B:T.119, B:H.230, B:R.231 Salt bridges: B:H.230, B:R.231, B:R.231 Metal complexes: B:H.230, B:H.245 HEC.19: 22 residues within 4Å: Chain B: C.114, I.117, I.183, S.193, F.195, T.196, R.199, H.200, S.203, L.204, R.207, Q.266, C.267, C.270, H.271, M.274, V.276, P.279, T.286, C.287 Ligands: HEC.17, HEC.20 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:I.117, B:I.183, B:F.195, B:L.204, B:L.204, B:V.276 Hydrogen bonds: B:T.196, B:S.203 Water bridges: B:T.196 Salt bridges: B:R.199, B:H.200, B:R.207 Metal complexes: B:H.200, B:H.271 HEC.20: 22 residues within 4Å: Chain B: I.183, D.184, A.185, L.186, A.187, D.188, K.189, Y.190, S.193, M.260, Y.263, H.264, C.267, M.268, H.271, R.280, D.281, D.283, C.284, C.287, H.288 Ligands: HEC.19 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:I.183, B:I.183, B:L.186, B:K.189, B:Y.190, B:Y.263, B:Y.263 Hydrogen bonds: B:L.186, B:D.188, B:K.189, B:Y.190 Metal complexes: B:H.264, B:H.288

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 6 residues within 4Å: Chain A: R.122, D.123, E.124 Chain B: K.121, S.232, P.233 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:K.121, B:K.121, B:S.232, B:S.232, A:E.124 Hydrophobic interactions: A:E.124

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 9 residues within 4Å: Chain A: K.121, R.231, S.232, P.233 Chain B: R.122, D.123, E.124, C.127 Ligands: HEC.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.122 Water bridges: B:E.124 GOL.21: 5 residues within 4Å: Chain A: R.256 Chain B: D.77, H.81 Ligands: HEC.7, HEC.16 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.256, A:R.256, B:D.77, B:D.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bento, I. et al., Redox-Bohr and Other Cooperativity Effects in the Nine-Heme Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774: Crystallographic and Modeling Studies. J.Biol.Chem. (2003)

Release Date

2003-09-18

Peptides

NINE HEME CYTOCHROME C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NINE HEME CYTOCHROME C

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